Integrated analysis of long non-coding RNA and mRNA expression in endometrial stromal cells induced by poly (I:C) identifies immune response genes

Abstract Background The uterus of an animal is relatively easily infected by pathogenic microorganisms, which can cause serious reproductive disorders and economic loss to animal husbandry. The presence of long noncoding RNA (lncRNA) is closely related to many diseases. Poly(I:C) is a synthetic double-stranded RNA that is often used as a substitute for dsRNA viral infection. In this study, we analyzed the mRNA and lncRNA expression profiles of in vitro cultured rabbit endometrial stromal cells (ESCs) after poly(I:C)-induction, to explore the role of these RNAs in the immune response. Results We identified 10,927 lncRNAs and 20,494 mRNAs, of which 291 lncRNAs and 1311 mRNAs were significantly differentially expressed (DE) between the control and poly(I:C) groups ( p <0.05). GO and KEGG analysis showed that DE genes and target genes of DE lncRNAs were enriched in relation to the occurrence of various diseases, development of tissues and organs, metabolic processes, and the immune response. Moreover, these genes were also enriched in many pathways related to immune and inflammatory responses, such as the toll-like receptor and the NF-κB and Jak-STAT signaling pathways. Co-expression analysis of lncRNA and mRNA revealed that there were significant relationships between a number of lncRNAs including MSTRG.153189.1, MSTRG.102664.8, MSTRG.39626.1, MSTRG.68469.1, MSTRG.137189.4, MSTRG.32118.5 and MSTRG.76080.1, and the immune system genes, CCL2, CCL5, IL-1, IL-6, IFN and ISG15, which suggested that lncRNAs in ESCs might be involved in regulation of the immune response to poly(I:C) through genes related to immune signaling pathways. Conclusions Our results provide both transcriptomic and epigenetic insights into the immune response of uterine cells to dsRNA virus infection. Comprehensive lncRNA and mRNA transcriptomes in rabbit ESCs exposed to poly(I:C) were profiled. Co-expression analysis identified an integrated lncRNA-mRNA interaction network, implying that key genes or lncRNAs exerted critical influences on the immune response to virus infection.